INITStepDesc

0001 classdef INITStepDesc
0002 % Describes a step in the ftINIT algorithm. A cell array of objects of this
0003 % class is used as input to ftINIT to specify how the algorithm should be run.
0004    properties
0005       PosRevOff
0006       AllowMetSecr
0007       HowToUsePrevResults %'ignore', 'exclude', 'essential'
0008       RxnsToIgnoreMask %Specifies reactions to leave outside the problem in
0009                        %the MILP.
0010                        % [b1,b2,b3,b4,b5,b6,b7,b8], bx is either 0 or 1,
0011                        % where 1 means that the group is excluded.
0012                        % b1 - Exchange rxns
0013                        % b2 - Import rxns without GPRs (from s into the cell)
0014                        % b3 - Simple transport reactions without GPRs (moves one metabolite between compartments)
0015                        % b4 - Advanced transport reactions without GPRs (moves metabolites between compartments, more complex function such as antiporter)
0016                        % b5 - Spontaneous reactions
0017                        % b6 - Reactions in the s compartment without GPRs
0018                        % b7 - Customly specified rxns (sent in when generating prepData)
0019                        % b8 - All rxns without GPRs
0020 
0021       MetsToIgnore % Structure describing mets that can be removed from the model
0022                    % before running ftINIT, such as water etc.
0023                    % .simpleMets
0024                    %      .mets        Names of metabolites to remove
0025                    %      .compsToKeep Compartments for which metabolites should be kept.
0026       MILPParams %Cell array of MILPparams - dictates how many iterations that will be run in this step.
0027                  %Typically, MIPGap and TimeLimit is specified
0028       AbsMIPGaps %If the objective is close to zero, a percentage of that is very small.
0029                  %Therefore, also set an absolut value for this (typically 10 or 20).
0030                  %For practical reasons, the first number is not used
0031    end
0032    methods
0033       function obj = INITStepDesc(posRevOff_, AllowMetSecr_, howToUsePrevResults_, rxnsToIgnoreMask_, metsToIgnore_, MILPParams_, absMIPGaps_)
0034          if nargin > 0
0035             obj.PosRevOff = posRevOff_;
0036          else
0037             obj.PosRevOff = false;
0038          end
0039          if nargin > 1
0040             obj.AllowMetSecr = AllowMetSecr_;
0041          else
0042             obj.AllowMetSecr = false;
0043          end
0044          if nargin > 2
0045             obj.HowToUsePrevResults = howToUsePrevResults_;
0046          else
0047             obj.HowToUsePrevResults = 'essential';
0048          end
0049          if nargin > 3
0050             obj.RxnsToIgnoreMask = rxnsToIgnoreMask_;
0051          else
0052             obj.RxnsToIgnoreMask = [1;0;0;0;0;0;0;0];
0053          end
0054          if nargin > 4
0055             obj.MetsToIgnore = metsToIgnore_;
0056          else
0057             obj.MetsToIgnore = [1;0;0;0;0;0;0;0];
0058          end
0059          if nargin > 5
0060             obj.MILPParams = MILPParams_;
0061          else
0062             params = struct();
0063             params.TimeLimit = 5000;
0064             params.MIPGap = 0.0004;            
0065             obj.MILPParams = {params};
0066          end
0067          
0068          if nargin > 6
0069             obj.AbsMIPGaps = absMIPGaps_;
0070          else
0071             obj.AbsMIPGaps = 10;            
0072          end
0073       end
0074    end
0075 end